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Fluorine in PDB 3rjh: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site, PDB code: 3rjh was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.35 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.530, 79.910, 55.460, 90.00, 108.04, 90.00
R / Rfree (%) 20.4 / 25.9

Other elements in 3rjh:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site (pdb code 3rjh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site, PDB code: 3rjh:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3rjh

Go back to Fluorine Binding Sites List in 3rjh
Fluorine binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:12.3
occ:1.00
 F1A A:6CF401 0.0 12.3 1.0
C3A A:6CF401 1.3 17.2 1.0
F2A A:6CF401 2.2 17.1 1.0
P2 A:6CF401 2.5 13.6 1.0
P1 A:6CF401 2.5 18.3 1.0
O1B A:6CF401 2.7 14.0 1.0
O5' A:6CF401 3.0 16.1 1.0
O A:HOH515 3.0 20.3 1.0
O2A A:6CF401 3.1 16.2 1.0
O3B A:6CF401 3.4 15.8 1.0
C3' A:6CF401 3.5 18.3 1.0
C5' A:6CF401 3.6 18.3 1.0
O2B A:6CF401 3.7 9.2 1.0
O1A A:6CF401 3.8 11.4 1.0
C6 A:6CF401 3.8 17.0 1.0
O3' A:6CF401 3.9 17.6 1.0
C4' A:6CF401 4.0 13.0 1.0
O A:HOH655 4.1 37.4 1.0
C5 A:6CF401 4.3 15.3 1.0
O1G A:6CF401 4.4 15.9 1.0
P3 A:6CF401 4.5 22.7 1.0
CB A:ASP276 4.6 22.6 1.0
O4' A:6CF401 4.6 16.4 1.0
C2' A:6CF401 4.6 16.7 1.0
CG A:ASP276 4.7 27.1 1.0
MG A:MG402 4.7 15.2 1.0
N1 A:6CF401 4.7 16.1 1.0
O A:HOH645 4.7 31.7 1.0
OD2 A:ASP276 4.7 28.1 1.0
N A:ASP276 4.8 21.0 1.0
C1' A:6CF401 4.9 15.3 1.0
O2G A:6CF401 5.0 19.9 1.0

Fluorine binding site 2 out of 2 in 3rjh

Go back to Fluorine Binding Sites List in 3rjh
Fluorine binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG:Da at Primer Terminus and Dg:Dcmp(CF2)Ppin the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:17.1
occ:1.00
 F2A A:6CF401 0.0 17.1 1.0
C3A A:6CF401 1.3 17.2 1.0
F1A A:6CF401 2.2 12.3 1.0
P2 A:6CF401 2.5 13.6 1.0
P1 A:6CF401 2.5 18.3 1.0
O3B A:6CF401 2.6 15.8 1.0
O1G A:6CF401 2.8 15.9 1.0
P3 A:6CF401 2.9 22.7 1.0
O2A A:6CF401 2.9 16.2 1.0
O A:HOH645 3.1 31.7 1.0
O2G A:6CF401 3.2 19.9 1.0
O1A A:6CF401 3.2 11.4 1.0
O A:HOH504 3.4 15.4 1.0
O2B A:6CF401 3.5 9.2 1.0
O1B A:6CF401 3.5 14.0 1.0
MG A:MG402 3.8 15.2 1.0
O5' A:6CF401 3.9 16.1 1.0
O A:HOH599 4.2 45.5 1.0
O A:HOH655 4.3 37.4 1.0
O A:HOH515 4.4 20.3 1.0
O3G A:6CF401 4.4 16.9 1.0
O A:HOH505 4.6 19.4 1.0
C5' A:6CF401 4.6 18.3 1.0

Reference:

V.K.Batra, D.D.Shock, W.A.Beard, C.E.Mckenna, S.H.Wilson. Binary Complex Crystal Structure of Dna Polymerase Beta Reveals Multiple Conformations of the Templating 8-Oxoguanine Lesion Proc.Natl.Acad.Sci.Usa V. 109 113 2012.
ISSN: ISSN 0027-8424
PubMed: 22178760
DOI: 10.1073/PNAS.1112235108
Page generated: Wed Jul 31 22:20:04 2024

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